Brand  (β version)

PDB ID: 6H4O

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Ligands
Code Name Style Show Link
ZN Zinc ion PoSSuM
FQH 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-D]pyrimidin-4-one PoSSuM
GOL Glycerol PoSSuM
CL Chloride ion PoSSuM
Non-standard Residues
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Structure summary

Code : 6H4O   PDBj   RCSB PDB   PDBe
Header : OXIDOREDUCTASE
Title : Crystal structure of human KDM4A in complex with compound 18a
Release Data : 2019-06-12
Compound :
mol_id molecule chains synonym
1 Lysine-specific demethylase 4A A,B,C,D JmjC domain-containing histone demethylation protein 3A,Jumonji domain-containing protein 2A
ec: 1.14.11.-
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli BL21(DE3)  (taxid:469008)
gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677
expression_system_variant: Rosetta
expression_system_vector_type: Plasmid
Authors : Le Bihan, Y.V., van Montfort, R.L.M.
Keywords : Histone demethylase, Inhibitor, transcription, OXIDOREDUCTASE
Exp. method : X-RAY DIFFRACTION ( 2.25 Å )
Citation :

C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays.

Le Bihan, Y.V.,Lanigan, R.M.,Atrash, B.  et al.
(2019)  Eur.J.Med.Chem.  177 : 316 - 337

PubMed: 31158747
DOI: 10.1016/j.ejmech.2019.05.041

Reaction

Chain : A, B, C, D
UniProt : O75164 (KDM4A_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + 2 2- oxoglutarate + 2 O2 = N(6)-methyl-L-lysyl(9)-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2 1.14.11.66 PubMed:16603238
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N(6),N(6),N(6)-trimethyl-L-lysyl(36)-[histone H3] + 2 2- oxoglutarate + 2 O2 = N(6)-methyl-L-lysyl(36)-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2 1.14.11.69 PubMed:16603238
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Cofactor: Evidence: Note:
Fe(2+) ECO:0000269 | PubMed:16603238
Binds 1 Fe(2+) ion per subunit.